The subject of the clause is ho logos (the word) and theos (God) is what the logos was. Word order in Greek does not affect subject onbject relationships like it does in English. However word order in Greek DOES signify emphasis and importance.
Also, word order in older English did not have the same extent of control over subject object relationship that it does in current English. And even in modern English word order is not the final word on the subject. (Cool, a DOUBLE pun in one phrase! lol)
For example, consider the following statement: "The life of the party was Suzy." Which is the subject? The life of the party? It appears so, yet it is entirely possible that Suzy is actually the subject. As more clearly illustrated lin this other example: "A brave man was Hector." Which is saying Hector was a brave man, not that some random brave guy happened to be named Hector.
In such cases the object is seen to have a dual purpose. One is to specify what is being said of the subject (that Suzy is the life of the party, or that Hector is in fact a brave man). Two, and this is important to note, special attention is being drawn to the object as being descriptive or qualitative. Saying Hector was a brave man identifies him as a brave man, but saying "A brave man was Hector" draws special attention to Hector's qualities as a brave man. It's a case of emphasis or focus.
Regarding
John 1:1, theos en ho logos is saying the word was God, but places special emphasis on the deific or divine quality of the logos. The word is still the subject but the EMPHASIS has shifted to God being that which the word was.
Older English translations kept the word order (And God was the Word) to keep that same emphasis, along the same lines as saying "A brave man was Hector". In fact, drop "brave" and say it like this: A
MAN was Hector. In other words Hector was a "real man, a superlative man, a definitive man". The emphasis being man although the subject is Hector.
And
GOD was the Word... This is not trying to say God existed as the Word as much as it is trying to empasize that the Word was nothing less than GOD.